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comparison cuff_macros.xml @ 3:9f243677c4c6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
author devteam
date Tue, 07 Feb 2017 18:41:04 -0500
parents 12aeae6d8587
children 0232f19d300f
comparison
equal deleted inserted replaced
2:12aeae6d8587 3:9f243677c4c6
26 <option value="CONDITION_LIST">List of single replicate conditions</option> 26 <option value="CONDITION_LIST">List of single replicate conditions</option>
27 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option> 27 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option>
28 </param> 28 </param>
29 <when value="BAM"> 29 <when value="BAM">
30 <repeat name="conditions" title="Condition" min="2"> 30 <repeat name="conditions" title="Condition" min="2">
31 <param name="name" title="Condition name" type="text" label="Name"/> 31 <param name="name" label="Condition name" type="text"/>
32 <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/> 32 <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/>
33 </repeat> 33 </repeat>
34 </when> 34 </when>
35 <when value="CXB"> 35 <when value="CXB">
36 <repeat name="conditions" title="Condition" min="2"> 36 <repeat name="conditions" title="Condition" min="2">
37 <param name="name" title="Condition name" type="text" label="Name"/> 37 <param name="name" label="Condition name" type="text"/>
38 <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/> 38 <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/>
39 </repeat> 39 </repeat>
40 </when> 40 </when>
41 <when value="CONDITION_LIST"> 41 <when value="CONDITION_LIST">
42 <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list" /> 42 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />
43 </when> 43 </when>
44 <when value="CONDITION_REPLICATE_LIST"> 44 <when value="CONDITION_REPLICATE_LIST">
45 <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list:list" /> 45 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" />
46 </when> 46 </when>
47 </conditional> 47 </conditional>
48 </xml> 48 </xml>
49 <token name="@CONDITION_SAMPLES@"> 49 <token name="@CONDITION_SAMPLES@">
50 #if $in_type.set_in_type in ['BAM', 'CXB'] 50 #if $in_type.set_in_type in ['BAM', 'CXB']
51 #for $condition in $in_type.conditions: 51 #for $condition in $in_type.conditions:
52 #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] ) 52 #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] )
53 $samples 53 '$samples'
54 #end for 54 #end for
55 #elif $in_type.set_in_type == 'CONDITION_LIST' 55 #elif $in_type.set_in_type == 'CONDITION_LIST'
56 #for $sample in $in_type.conditions: 56 #for $sample in $in_type.conditions:
57 $sample 57 '$sample'
58 #end for 58 #end for
59 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' 59 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST'
60 #for $condition_list in $in_type.conditions: 60 #for $condition_list in $in_type.conditions:
61 #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] ) 61 #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] )
62 $samples 62 '$samples'
63 #end for 63 #end for
64 #end if 64 #end if
65 </token> 65 </token>
66 <token name="@CONDITION_LABELS@"> 66 <token name="@CONDITION_LABELS@">
67 #import re 67 #import re
79 </repeat> 79 </repeat>
80 </xml> 80 </xml>
81 <token name="@CUFFLINKS_GTF_INPUTS@"> 81 <token name="@CUFFLINKS_GTF_INPUTS@">
82 ## Inputs. 82 ## Inputs.
83 #for $input_file in $inputs: 83 #for $input_file in $inputs:
84 "${input_file}" 84 '${input_file}'
85 #end for 85 #end for
86 #for $additional_input in $additional_inputs: 86 #for $additional_input in $additional_inputs:
87 #for $input_file in $additional_input.additional_inputs: 87 #for $input_file in $additional_input.additional_inputs:
88 "${input_file}" 88 '${input_file}'
89 #end for 89 #end for
90 #end for 90 #end for
91 </token> 91 </token>
92 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token> 92 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
93 </macros> 93 </macros>